Slamf1 (signaling lymphocytic activation molecule family member 1) - Rat Genome Database

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Gene: Slamf1 (signaling lymphocytic activation molecule family member 1) Rattus norvegicus
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Symbol: Slamf1
Name: signaling lymphocytic activation molecule family member 1
RGD ID: 1560634
Description: Predicted to enable several functions, including SH2 domain binding activity; identical protein binding activity; and virus receptor activity. Predicted to be involved in several processes, including natural killer cell activation; positive regulation of MAPK cascade; and regulation of cytokine production. Predicted to act upstream of or within leukocyte chemotaxis involved in inflammatory response; positive regulation of leukocyte chemotaxis; and regulation of vesicle fusion. Predicted to be located in cell surface and phagocytic vesicle. Predicted to be active in external side of plasma membrane. Orthologous to human SLAMF1 (signaling lymphocytic activation molecule family member 1); PARTICIPATES IN measles pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC498286; RGD1560634; signaling lymphocytic activation molecule; similar to signaling lymphocytic activation molecule
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81386,802,708 - 86,837,890 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1386,802,708 - 86,837,890 (+)EnsemblGRCr8
mRatBN7.21384,270,316 - 84,305,497 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,270,316 - 84,305,497 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1386,773,651 - 86,808,837 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01388,173,933 - 88,209,121 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,359,002 - 85,394,197 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,184,545 - 90,219,170 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,184,569 - 90,219,217 (+)Ensemblrn6Rnor6.0
Rnor_5.013101,446,883 - 101,481,363 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41387,769,569 - 87,804,963 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1383,882,850 - 83,917,969 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9126961   PMID:11477403   PMID:16317102   PMID:18031695   PMID:18971422   PMID:20231852   PMID:20458337   PMID:20660734   PMID:21217702   PMID:21982860   PMID:22493499   PMID:22960654  
PMID:23528453   PMID:25799045   PMID:26095368   PMID:39260308  


Genomics

Comparative Map Data
Slamf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81386,802,708 - 86,837,890 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1386,802,708 - 86,837,890 (+)EnsemblGRCr8
mRatBN7.21384,270,316 - 84,305,497 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,270,316 - 84,305,497 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1386,773,651 - 86,808,837 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01388,173,933 - 88,209,121 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,359,002 - 85,394,197 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,184,545 - 90,219,170 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,184,569 - 90,219,217 (+)Ensemblrn6Rnor6.0
Rnor_5.013101,446,883 - 101,481,363 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41387,769,569 - 87,804,963 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1383,882,850 - 83,917,969 (+)NCBICelera
Cytogenetic Map13q24NCBI
SLAMF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381160,608,106 - 160,647,044 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1160,608,100 - 160,647,044 (-)Ensemblhg38GRCh38
GRCh371160,577,896 - 160,616,834 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,846,513 - 158,883,493 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341157,392,961 - 157,429,942NCBI
Celera1133,648,634 - 133,685,810 (-)NCBICelera
Cytogenetic Map1q23.3NCBI
HuRef1131,936,108 - 131,973,275 (-)NCBIHuRef
CHM1_11161,975,242 - 162,012,420 (-)NCBICHM1_1
T2T-CHM13v2.01159,745,198 - 159,784,140 (-)NCBIT2T-CHM13v2.0
Slamf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,594,700 - 171,628,752 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1171,594,695 - 171,628,752 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381171,767,131 - 171,801,184 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1171,767,127 - 171,801,184 (+)Ensemblmm10GRCm38
MGSCv371173,697,263 - 173,731,315 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361173,603,832 - 173,636,936 (+)NCBIMGSCv36mm8
Celera1174,623,305 - 174,657,749 (+)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.54NCBI
Slamf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546812,334,307 - 12,370,334 (-)Ensembl
ChiLan1.0NW_00495546812,336,744 - 12,383,917 (-)NCBIChiLan1.0ChiLan1.0
SLAMF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2189,203,016 - 89,242,333 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1188,943,220 - 88,982,359 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01135,963,748 - 136,002,982 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11139,888,596 - 139,925,461 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1139,888,772 - 139,925,461 (-)EnsemblpanPan2panpan1.1
SLAMF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13821,653,801 - 21,685,408 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3821,653,487 - 21,685,408 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3821,726,592 - 21,758,187 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03821,770,801 - 21,804,397 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3821,770,907 - 21,802,603 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13821,658,262 - 21,689,651 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03822,072,127 - 22,103,678 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03822,481,891 - 22,513,458 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slamf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050586,661,580 - 6,698,569 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493674055,941 - 92,100 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493674055,941 - 92,100 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLAMF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl489,870,539 - 89,908,231 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1489,870,359 - 89,907,114 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2497,762,763 - 97,799,248 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLAMF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1203,282,862 - 3,320,943 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl203,282,774 - 3,322,926 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660382,326,973 - 2,367,237 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slamf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624794627,906 - 661,257 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Slamf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11050,923,741 - 50,959,411 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Slamf1
129 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:605
Count of miRNA genes:272
Interacting mature miRNAs:340
Transcripts:ENSRNOT00000033868
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134863963493639634Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133721624190057603Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1338975045103588154Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)1371610804109350286Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1383286150109350286Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137161080489333251Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134874981487285480Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137161080489333251Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137298450699745408Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1367635937109350286Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137161080489333251Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13742179187286911Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
724564Uae11Urinary albumin excretion QTL 115.7urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)134735425894285672Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)1365613454109350286Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1368983334109350286Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136242459288113509Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1367635937109350286Rat
1576318Schws5Schwannoma susceptibility QTL 50.0351nervous system integrity trait (VT:0010566)post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)1364497900109350286Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1311081740103588154Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13600200888706694Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1364375743109350286Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131103588154Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1367635937109350286Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 42 136 82 81 50 92 50 6 302 166 10 109 63 83 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000082393   ⟹   ENSRNOP00000072438
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1386,802,708 - 86,837,890 (+)Ensembl
mRatBN7.2 Ensembl1384,270,316 - 84,305,497 (+)Ensembl
Rnor_6.0 Ensembl1390,184,569 - 90,219,217 (+)Ensembl
RefSeq Acc Id: NM_001109078   ⟹   NP_001102548
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81386,802,708 - 86,837,890 (+)NCBI
mRatBN7.21384,270,316 - 84,305,497 (+)NCBI
Rnor_6.01390,184,545 - 90,219,170 (+)NCBI
Rnor_5.013101,446,883 - 101,481,363 (+)NCBI
RGSC_v3.41387,769,569 - 87,804,963 (+)RGD
Celera1383,882,850 - 83,917,969 (+)RGD
Sequence:
RefSeq Acc Id: XM_039090985   ⟹   XP_038946913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81386,811,291 - 86,837,305 (+)NCBI
mRatBN7.21384,278,899 - 84,305,380 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102548 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946913 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94664 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072438
  ENSRNOP00000072438.1
RefSeq Acc Id: NP_001102548   ⟸   NM_001109078
- Peptide Label: precursor
- UniProtKB: D3ZAD7 (UniProtKB/TrEMBL),   A6JG08 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072438   ⟸   ENSRNOT00000082393
RefSeq Acc Id: XP_038946913   ⟸   XM_039090985
- Peptide Label: isoform X1
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAD7-F1-model_v2 AlphaFold D3ZAD7 1-345 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699017
Promoter ID:EPDNEW_R9540
Type:single initiation site
Name:Slamf1_1
Description:signaling lymphocytic activation molecule family member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01390,184,573 - 90,184,633EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560634 AgrOrtholog
BioCyc Gene G2FUF-17341 BioCyc
Ensembl Genes ENSRNOG00000059073 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082393 ENTREZGENE
  ENSRNOT00000082393.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CD2/SLAM_rcpt UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Sig_lymph_act_molc_N UniProtKB/TrEMBL
KEGG Report rno:498286 UniProtKB/TrEMBL
NCBI Gene 498286 ENTREZGENE
PANTHER SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE UniProtKB/TrEMBL
  SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE UniProtKB/TrEMBL
Pfam SLAM UniProtKB/TrEMBL
PhenoGen Slamf1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000059073 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A6JG08 ENTREZGENE, UniProtKB/TrEMBL
  D3ZAD7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Slamf1  signaling lymphocytic activation molecule family member 1  RGD1560634_predicted  similar to signaling lymphocytic activation molecule (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560634_predicted  similar to signaling lymphocytic activation molecule (predicted)  LOC498286  similar to signaling lymphocytic activation molecule  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498286  similar to signaling lymphocytic activation molecule      Symbol and Name status set to provisional 70820 PROVISIONAL